Dear Jesper,

The resting state data were collected as part as of a larger experimental protocol that also includes T1-weighted MRI, arterial spin labeling and diffusion tensor imaging. We acquired before DTI the blip-up-down data with different resolution.

I need to register the data to EPI and resample the data.

I used Topup to create my fieldmap, after registered it to EPI, and applytopup to EPI. But, the last step, applytopup, didn't work. I don't understand.

Julie

2014-12-06 1:59 GMT-08:00 Jesper Andersson <[log in to unmask]>:

Dear Julie,

> I tried to reduce distorsions for rs-fRMI. To do so, I apply topup. My fieldmap had a problem of header (resolution). I fixed that. After that, I registered my output into my T1.

I think this might be the crux. What do you mean by “registered my output into my T1”, and what do you mean by “my fieldmap”? Has the fieldmap been estimated using blip-up-down data, or is it a “classic” gradient echo fieldmap?

If it is the latter you should use fugue (or bbr) in order to apply it to your data. If it is the former you should use applytopup directly on your EPI data and after that register the corrected EPI images to your T1.

Jesper

> Then, I applied applytopup and got the following error: TOPUP::ApplyTopupException' what(): ApplyTopup:: msg=Invalid combination of phase-encode vectors for least-squares restoration.
> As explained on other messages, I used --method=jac.
> But, now I obtain this error:
> applytopup: /usr/include/boost/smart_ptr/shared_ptr.hpp:646: typename boost::detail::sp_dereference<T>::type boost::shared_ptr<T>::operator*() const [with T = BASISFIELD::splinefield; typename boost::detail::sp_dereference<T>::type = BASISFIELD::splinefield&]: Assertion `px != 0' failed.
> I don't understand this error. Can anyone help with this?
> Thanks,
> Julie